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sash: skip VCF2MAF when PCGR skipped for high-variant-count samples (#52) - #59
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When bolt PASS VCF exceeds 450k variants, select_pcgr_variants raises RuntimeError and PCGR is skipped. Mark pcgr_pass_vcf, pcgr_dir, and pcgr_report as optional so the process exits 0 and non-PCGR outputs (stats, AFs, counts) are still published for gpgr. Filter the VCF2MAF input channel to skip samples where pcgr_pass_vcf was not emitted. Closes #52
This was referenced Jul 17, 2026
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qclayssen
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Jul 31, 2026
…t samples BOLT_SMLV_SOMATIC_REPORT unconditionally moved output/pcgr/*.html, which does not exist when PCGR/VCF2MAF are skipped for samples exceeding the sash #59 variant-count cap (ADR-001) -- causing the whole process to hard-fail on exactly the samples that skip is meant to handle. Adds nf-test coverage: optional PCGR emits let the process exit 0 when skipped, and the vcf2maf_input_filter channel chain drops the skipped sample's null entry before it reaches VCF2MAF.
qclayssen
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Aug 7, 2026
Exercises the actual script: block against ghcr.io/umccr/bolt:0.3.2-pcgr, covering the mv output/pcgr/*.html guard fix (sash #59 / ADR-001) that stub-mode tests can't reach since -stub bypasses script: entirely.
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Summary
Part of sash 0.7.1 (bolt 0.3.1 → 0.3.2).
select_pcgr_variantsraisesRuntimeErrorand PCGR is skipped (bolt-side fix: Fix/52 pcgr skip high variant count bolt#32, merged intorelease/0.3.0/tagv0.3.2).pcgr_pass_vcf,pcgr_dir, andpcgr_reportasoptional: trueonBOLT_SMLV_SOMATIC_REPORTso the process exits 0 and non-PCGR outputs (stats, AFs, counts) still publish for gpgr.VCF2MAFinput channel to skip samples wherepcgr_pass_vcfwas not emitted.Related:
bcftools mergeguard, bolt change make hrd facultative for cancer report process #26)Closes #52.
Test plan
nextflow config .— parses cleanlynextflow run . --help— forces full DSL2 compilation of changed files, no syntax errorsnf-testexists forBOLT_SMLV_SOMATIC_REPORTor this part ofworkflows/sash.nf(known gap, noted in CHANGELOG) — not run against real cloud data as part of this PR